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Watanabe T, Soeda S, Endo Y, Okabe C, Sato T, Kamo N, Ueda M, Kojima M, Furukawa S, Nishigori H, Takahashi T, Fujimori K. Rare Hereditary Gynecological Cancer Syndromes. Int J Mol Sci 2022; 23:1563. [PMID: 35163487 PMCID: PMC8835983 DOI: 10.3390/ijms23031563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/04/2022] Open
Abstract
Hereditary cancer syndromes, which are characterized by onset at an early age and an increased risk of developing certain tumors, are caused by germline pathogenic variants in tumor suppressor genes and are mostly inherited in an autosomal dominant manner. Therefore, hereditary cancer syndromes have been used as powerful models to identify and characterize susceptibility genes associated with cancer. Furthermore, clarification of the association between genotypes and phenotypes in one disease has provided insights into the etiology of other seemingly different diseases. Molecular genetic discoveries from the study of hereditary cancer syndrome have not only changed the methods of diagnosis and management, but have also shed light on the molecular regulatory pathways that are important in the development and treatment of sporadic tumors. The main cancer susceptibility syndromes that involve gynecologic cancers include hereditary breast and ovarian cancer syndrome as well as Lynch syndrome. However, in addition to these two hereditary cancer syndromes, there are several other hereditary syndromes associated with gynecologic cancers. In the present review, we provide an overview of the clinical features, and discuss the molecular genetics, of four rare hereditary gynecological cancer syndromes; Cowden syndrome, Peutz-Jeghers syndrome, DICER1 syndrome and rhabdoid tumor predisposition syndrome 2.
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Affiliation(s)
- Takafumi Watanabe
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Shu Soeda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Yuta Endo
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Chikako Okabe
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Tetsu Sato
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Norihito Kamo
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Makiko Ueda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Manabu Kojima
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Shigenori Furukawa
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Hidekazu Nishigori
- Fukushima Medical Center for Children and Women, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan; (H.N.); (T.T.)
| | - Toshifumi Takahashi
- Fukushima Medical Center for Children and Women, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan; (H.N.); (T.T.)
| | - Keiya Fujimori
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
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Turri-Zanoni M, Gravante G, Castelnuovo P. Molecular Biomarkers in Sinonasal Cancers: New Frontiers in Diagnosis and Treatment. Curr Oncol Rep 2022; 24:55-67. [PMID: 35059992 PMCID: PMC8831338 DOI: 10.1007/s11912-021-01154-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Purpose of Review Sinonasal tumors are rare and heterogeneous diseases which pose challenges in diagnosis and treatment. Despite significant progress made in surgical, oncological, and radiotherapy fields, their prognosis still remains poor. Therefore, alternative strategies should be studied in order to refine diagnosis and improve patient care. Recent Findings In recent years, in-depth molecular studies have identified new biological markers, such as genetic abnormalities and epigenetic variations, which have allowed to refine diagnosis and predict prognosis. As a consequence, new histological entities have been described and specific subgroup stratifications within the well-known histotypes have been made possible. These discoveries have expanded indications for immunotherapy and targeted therapies in order to reduce tumor spread, thus representing a valuable implementation of standard treatments. Summary Recent findings in molecular biology have paved the way for better understanding and managing such rare and aggressive tumors. Although further efforts need to be made in this direction, expectations are promising.
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Shen M, Qi R, Ren J, Lv D, Yang H. Characterization With KRAS Mutant Is a Critical Determinant in Immunotherapy and Other Multiple Therapies for Non-Small Cell Lung Cancer. Front Oncol 2022; 11:780655. [PMID: 35070984 PMCID: PMC8766810 DOI: 10.3389/fonc.2021.780655] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a frequent type of cancer, which is mainly characterized clinically by high aggressiveness and high mortality. KRAS oncoprotein is the most common molecular protein detected in NSCLC, accounting for 25% of all oncogenic mutations. Constitutive activation of the KRAS oncoprotein triggers an intracellular cascade in cancer cells, leading to uncontrolled cell proliferation of cancer cells and aberrant cell survival states. The results of multiple clinical trials have shown that different KRAS mutation subtypes exhibit different sensitivities to different chemotherapy regimens. Meanwhile, anti-angiogenic drugs have shown differential efficacy for different subtypes of KRAS mutated lung cancer. It was explored to find if the specificity of the KRAS mutation subtype would affect PD-L1 expression, so immunotherapy would be of potential clinical value for the treatment of some types of KRAS mutations. It was discovered that the specificity of the KRAS mutation affected PD-L1, which opened up immunotherapy as a potential clinical treatment option. After several breakthrough studies, the preliminary test data of many early clinical trials showed that it is possible to directly inhibit KRAS G12C mutation, which has been proved to be a targeted treatment that is suitable for about 10%-12% of patients with advanced NSCLC, having a significant impact on the prolongation of their survival and the improvement of their quality of life. This article reviews the latest progress of treatments for NSCLC with KRAS mutation, in order to gain insight into the biological diversity of lung cancer cells and their potential clinical implications, thereby enabling individualized treatment for patients with KRAS-mutant NSCLC.
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Affiliation(s)
- Mo Shen
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Rongbin Qi
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Justin Ren
- Biological Sciences, Northwestern University, Evanston, Evanston, IL, United States
| | - Dongqing Lv
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Haihua Yang
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Radiation Oncology, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
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Liu X, Li Z, Wang Z, Liu F, Zhang L, Ke J, Xu X, Zhang Y, Yuan Y, Wei T, Shan Q, Chen Y, Huang W, Gao J, Wu N, Chen F, Sun L, Qiu Z, Deng Y, Wang X. Chromatin remodeling induced by ARID1A loss in lung cancer promotes glycolysis and confers JQ1 vulnerability. Cancer Res 2022; 82:791-804. [PMID: 34987057 DOI: 10.1158/0008-5472.can-21-0763] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/03/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
ARID1A is a key mammalian SWI/SNF complex subunit that is mutated in 5%-11% of lung cancers. Although recent studies have elucidated the mechanism underlying dysregulation of SWI/SNF complexes in cancers, the significance of ARID1A loss and its implications in lung cancers remain poorly defined. This study investigates how ARID1A loss affects initiation and progression of lung cancer. In genetically engineered mouse models bearing mutant Kras and a deficient Trp53 allele (KP), ARID1A loss (KPA) promoted lung tumorigenesis. Analysis of the transcriptome profiles of KP and KPA tumors suggested enhanced glycolysis following ARID1A loss, and expression of the glycolytic regulators Pgam1, Pkm, and Pgk1 was significantly increased in ARID1A-deficient lung tumors. Furthermore, ARID1A loss increased chromatin accessibility and enhanced HIF1α binding to the promoter regions of Pgam1, Pkm, and Pgk1. Loss of ARID1A in lung adenocarcinoma also resulted in loss of histone deacetylase 1 (HDAC1) recruitment, increasing acetylation of histone 4 lysine at the promoters of Pgam1, Pkm, and Pgk1 and subsequently enhancing BRD4-driven transcription of these genes. Metabolic analyses confirmed that glycolysis is enhanced in ARID1A-deficient tumors, and genetic or pharmacologic inhibition of glycolysis inhibited lung tumorigenesis in KPA mice. Treatment with the small molecule bromodomain and extra terminal protein (BET) inhibitor JQ1 compromised both initiation and progression of ARID1A-deficient lung adenocarcinoma. ARID1A negatively correlated with glycolysis-related genes in human lung adenocarcinoma. Overall, ARID1A loss leads to metabolic reprogramming that supports tumorigenesis but also confers a therapeutic vulnerability that could be harnessed to improve the treatment of ARID1A-deficient lung cancer.
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Affiliation(s)
- Xiaoyu Liu
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Li
- Department of Oncology, Xiangya Cancer Center Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders and Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Zhongmin Wang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital LuWan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Liu
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
| | - Linling Zhang
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
| | - Jingjing Ke
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
| | - Xu Xu
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuefang Zhang
- State Key Laboratory of Neuroscience, Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yiting Yuan
- State Key Laboratory of Neuroscience, Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qungang Shan
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital LuWan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjie Chen
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital LuWan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Huang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital LuWan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Gao
- Department of Oncology, Xiangya Cancer Center Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders and Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Nan Wu
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
| | - Fuliang Chen
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
| | - Lunquan Sun
- Department of Oncology, Xiangya Cancer Center Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders and Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Zilong Qiu
- State Key Laboratory of Neuroscience, Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yuezhen Deng
- Department of Oncology, Xiangya Cancer Center Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders and Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaojing Wang
- Anhui Province Key Laboratory of Clinical and Preclinical Research in Respiratory Disease, Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Bengbu Medical College, Anhui, China
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Haberecker M, Bühler MM, Mendieta AP, Guggenberger R, Arnold F, Markert E, Rechsteiner M, Zoche M, Britschgi C, Pauli C. Molecular and immunophenotypic characterization of SMARCB1 (INI1) - deficient intrathoracic Neoplasms. Mod Pathol 2022; 35:1860-1869. [PMID: 35864317 PMCID: PMC9708576 DOI: 10.1038/s41379-022-01133-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022]
Abstract
The switch/sucrose-non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeling complex that plays important roles in DNA repair, transcription and cell differentiation. This complex consists of multiple subunits and is of particular interest in thoracic malignancies due to frequent subunit alteration of SMARCA4 (BRG1). Much less is known about SMARCB1 (INI1) deficient intrathoracic neoplasms, which are rare, often misclassified and understudied. In a retrospective analysis of 1479 intrathoracic malignant neoplasms using immunohistochemistry for INI1 (SMARCB1) on tissue micro arrays (TMA) and a search through our hospital sarcoma database, we identified in total nine intrathoracic, INI1 deficient cases (n = 9). We characterized these cases further by additional immunohistochemistry, broad targeted genomic analysis, methylation profiling and correlated them with clinical and radiological data. This showed that genomic SMARCB1 together with tumor suppressor alterations drive tumorigenesis in some of these cases, rather than epigenetic changes such as DNA methylation. A proper diagnostic classification, however, remains challenging. Intrathoracic tumors with loss or alteration of SMARCB1 (INI1) are highly aggressive and remain often underdiagnosed due to their rarity, which leads to false diagnostic interpretations. A better understanding of these tumors and proper diagnosis is important for better patient care as clinical trials and more targeted therapeutic options are emerging.
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Affiliation(s)
- Martina Haberecker
- grid.412004.30000 0004 0478 9977Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Marco Matteo Bühler
- grid.412004.30000 0004 0478 9977Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Alicia Pliego Mendieta
- grid.412004.30000 0004 0478 9977Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Roman Guggenberger
- grid.412004.30000 0004 0478 9977Department of Radiology, University Hospital Zurich, Zurich, Switzerland
| | - Fabian Arnold
- grid.412004.30000 0004 0478 9977Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Eva Markert
- grid.413349.80000 0001 2294 4705Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Markus Rechsteiner
- grid.412004.30000 0004 0478 9977Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Martin Zoche
- grid.412004.30000 0004 0478 9977Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Christian Britschgi
- grid.412004.30000 0004 0478 9977Department of Medical Oncology and Hematology, University Hospital Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland. .,University Zurich, Zurich, Switzerland.
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Mardinian K, Adashek JJ, Botta GP, Kato S, Kurzrock R. SMARCA4: Implications of an Altered Chromatin-Remodeling Gene for Cancer Development and Therapy. Mol Cancer Ther 2021; 20:2341-2351. [PMID: 34642211 PMCID: PMC8643328 DOI: 10.1158/1535-7163.mct-21-0433] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 01/04/2023]
Abstract
The SWI/SNF chromatin remodeling complex, via nucleosome topology modulation, regulates transcription. The SMARCA4 (BRG1) subunit codes for the ATPase energy engine of the SWI/SNF complex. SMARCA4 is a tumor suppressor that is aberrant in ∼5% to 7% of human malignancies. Class I SMARCA4 alterations (truncating mutations, fusions, and homozygous deletion) lead to loss of function whereas class II alterations (missense mutations) have a dominant negative/gain-of-function effect and/or loss-of function. SMARCA4 alterations typify the ultra-rare small cell carcinomas of the ovary hypercalcemic type (SCCOHT) and SMARCA4-deficient thoracic and uterine sarcomas; they are also found in a subset of more common tumors, for example, lung, colon, bladder, and breast carcinomas. Germline variants in the SMARCA4 gene lead to various hereditary conditions: rhabdoid tumor predisposition syndrome-2 (RTPS2), characterized by loss-of-function alterations and aggressive rhabdoid tumors presenting in infants and young children; and Coffin-Siris syndrome, characterized by dominant negative/gain-of function alterations and developmental delays, microcephaly, unique facies, and hypoplastic nails of the fifth fingers or toes. A minority of rhabdoid tumors have a germline SMARCA4 variant as do >40% of women with SCCOHT. Importantly, immune checkpoint blockade has shown remarkable, albeit anecdotal, responses in SCCOHT. In addition, there is ongoing research into BET, EZH2, HDAC, CDK4/6, and FGFR inhibitors, as well as agents that might induce synthetic lethality via DNA damage repair impairment (ATR inhibitors and platinum chemotherapy), or via the exploitation of mitochondrial oxidative phosphorylation inhibitors or AURKA inhibitors, in SMARCA4-aberrant cancers.
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Affiliation(s)
- Kristina Mardinian
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Jacob J Adashek
- Department of Internal Medicine, University of South Florida, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
| | - Gregory P Botta
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Shumei Kato
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California. .,WIN Consortium, Paris, France
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SMARCA4 Depletion Induces Cisplatin Resistance by Activating YAP1-Mediated Epithelial-to-Mesenchymal Transition in Triple-Negative Breast Cancer. Cancers (Basel) 2021; 13:cancers13215474. [PMID: 34771636 PMCID: PMC8582548 DOI: 10.3390/cancers13215474] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary SMARCA4 mutations were over-representative in cisplatin resistance and metastatic triple-negative breast cancer (TNBC). Additionally, SMARCA4 inactivation induced the mesenchymal-like subtype TNBC. The epithelial-to-mesenchymal transition and Hippo-YAP/TAZ pathways were activated in SMARCA4 inactivation samples of both SMARCA4 knockout cell lines and TNBC patients. In SMARCA4 knockout cells, the YAP1 inhibitor verteporfin suppressed YAP1 target genes. This study depicts the clinical importance of SMARCA4 depletion in TNBC and suggests YAP/TAZ as a novel target for cisplatin-resistant patients. Abstract The role of SMARCA4, an ATPase subunit of the SWI/SNF chromatin remodeling complex, in genomic organization is well studied in various cancer types. However, its oncogenic role and therapeutic implications are relatively unknown in triple-negative breast cancer (TNBC). We investigated the clinical implication and downstream regulation induced by SMARCA4 inactivation using large-scale genome and transcriptome profiles. Additionally, SMARCA4 was knocked out in MDA-MB-468 and MDA-MB-231 using CRISPR/Cas9 to identify gene regulation and a targetable pathway. First, we observed an increase in SMARCA4 mutations in cisplatin resistance and metastasis in TNBC patients. Its inactivation was associated with the mesenchymal-like (MSL) subtype. Gene expression analysis showed that the epithelial-to-mesenchymal transition (EMT) pathway was activated in SMARCA4-deficient patients. Next, the Hippo pathway was activated in the SMARCA4 inactivation group, as evidenced by the higher CTNNB1, TGF-β, and YAP1 oncogene signature scores. In SMARCA4 knockout cells, EMT was upregulated, and the cell line transcriptome changed from the SL to the MSL subtype. SMARCA4 knockout cells showed cisplatin resistance and Hippo-YAP/TAZ target gene activation. The YAP1 inhibitor verteporfin suppressed the expression of YAP1 target genes, and decreased cell viability and invasiveness on SMARCA4 knockout cells. SMARCA4 inactivation in TNBC endowed the resistance to cisplatin via EMT activation. The YAP1 inhibitor could become a novel strategy for patients with SMARCA4-inactivated TNBC.
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Peng L, Li J, Wu J, Xu B, Wang Z, Giamas G, Stebbing J, Yu Z. A Pan-Cancer Analysis of SMARCA4 Alterations in Human Cancers. Front Immunol 2021; 12:762598. [PMID: 34675941 PMCID: PMC8524462 DOI: 10.3389/fimmu.2021.762598] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 01/04/2023] Open
Abstract
Background SMARCA4, the essential ATPase subunit of SWI/SNF chromatin remodeling complex, regulates transcription through the control of chromatin structure and is increasingly thought to play significant roles in human cancers. This study aims to explore the potential role of SMARCA4 with a view to providing insights on pathologic mechanisms implicated here. Methods The potential roles of SMARCA4 in different tumors were explored based on The Cancer Genome Atlas (TCGA), Genotype-tissue expression (GTEx), Tumor Immune Estimation Resource (TIMER), and Gene Set Enrichment Analysis (GSEA) datasets. The expression difference, mutation and phosphorylation status, survival, pathological stage, DNA methylation, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), tumor microenvironment (TME), and immune cell infiltration related to SMARCA4 were analyzed. Results High expression levels of SMARCA4 were observed in most cancer types. SMARCA4 expression in tumor samples correlates with poor overall survival in several cancers. Lung adenocarcinoma cases with altered SMARCA4 showed a poorer prognosis. Enhanced phosphorylation levels of S613, S695, S699, and S1417 were observed in several tumors, including breast cancer. SMARCA4 correlated with tumor immunity and associated with different immune cells and genes in different cancer types. TMB, MSI, MMR, and DNA methylation correlated with SMARCA4 dysregulation in cancers. SMARCA4 expression was negatively associated with CD8+ T-cell infiltration in several tumors. Furthermore, the SWI/SNF superfamily-type complex and ATPase complex may be involved in the functional mechanisms of SMARCA4, albeit these data require further confirmation. Conclusions Our study offers a comprehensive understanding of the oncogenic roles of SMARCA4 across different tumors. SMARCA4 may correlate with tumor immunity.
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Affiliation(s)
- Ling Peng
- Department of Respiratory Disease, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jisheng Li
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Wu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Zhentao Yu
- Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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Concepcion CP, Ma S, LaFave LM, Bhutkar A, Liu M, DeAngelo LP, Kim JY, Del Priore I, Schoenfeld AJ, Miller M, Kartha VK, Westcott PMK, Sanchez-Rivera FJ, Meli K, Gupta M, Bronson RT, Riely GJ, Rekhtman N, Rudin CM, Kim CF, Regev A, Buenrostro JD, Jacks T. SMARCA4 inactivation promotes lineage-specific transformation and early metastatic features in the lung. Cancer Discov 2021; 12:562-585. [PMID: 34561242 DOI: 10.1158/2159-8290.cd-21-0248] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/30/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022]
Abstract
SMARCA4/BRG1 encodes for one of two mutually exclusive ATPases present in mammalian SWI/SNF chromatin remodeling complexes and is frequently mutated in human lung adenocarcinoma. However, the functional consequences of SMARCA4 mutation on tumor initiation, progression, and chromatin regulation in lung cancer remain poorly understood. Here, we demonstrate that loss of Smarca4 sensitizes CCSP+ cells within the lung in a cell-type dependent fashion to malignant transformation and tumor progression, resulting in highly advanced dedifferentiated tumors and increased metastatic incidence. Consistent with these phenotypes, Smarca4-deficient primary tumors lack lung lineage transcription factor activities and resemble a metastatic cell state. Mechanistically, we show that Smarca4 loss impairs the function of all three classes of SWI/SNF complexes, resulting in decreased chromatin accessibility at lung lineage motifs and ultimately accelerating tumor progression. Thus, we propose that the SWI/SNF complex - via Smarca4 - acts as a gatekeeper for lineage-specific cellular transformation and metastasis during lung cancer evolution.
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Affiliation(s)
- Carla P Concepcion
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | - Lindsay M LaFave
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Arjun Bhutkar
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology
| | - Manyuan Liu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Lydia P DeAngelo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | - Isabella Del Priore
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | - Manon Miller
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | - Peter M K Westcott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | - Kevin Meli
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | | | | | | | - Charles M Rudin
- Druckenmiller Center for Lung Cancer Research and Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center
| | - Carla F Kim
- Stem Cell Program, Harvard University, Boston Children's Hospital
| | | | | | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
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60
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Yao H, Huo L, Ping N, Liu H, Li H, Ding Z, Shen H, Xie J, Qiu Q, Ma L, Jiang A, Wang Q, Wu D, Yang X, Song Y, Chen S. Recurrent mutations in multiple components of the SWI/SNF complex in myelodysplastic syndromes and acute myeloid leukaemia. Br J Haematol 2021; 196:441-444. [PMID: 34535894 DOI: 10.1111/bjh.17795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Hong Yao
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, P.R. China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Li Huo
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Nana Ping
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Hong Liu
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Zixuan Ding
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Hongjie Shen
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Jundan Xie
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Qiaocheng Qiu
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Liang Ma
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Airui Jiang
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Qian Wang
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Depei Wu
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Xiaofei Yang
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
| | - Yaohua Song
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, P.R. China
| | - Suning Chen
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.,Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P.R. China
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61
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Xue Y, Morris JL, Yang K, Fu Z, Zhu X, Johnson F, Meehan B, Witkowski L, Yasmeen A, Golenar T, Coatham M, Morin G, Monast A, Pilon V, Fiset PO, Jung S, Gonzalez AV, Camilleri-Broet S, Fu L, Postovit LM, Spicer J, Gotlieb WH, Guiot MC, Rak J, Park M, Lockwood W, Foulkes WD, Prudent J, Huang S. SMARCA4/2 loss inhibits chemotherapy-induced apoptosis by restricting IP3R3-mediated Ca 2+ flux to mitochondria. Nat Commun 2021; 12:5404. [PMID: 34518526 PMCID: PMC8438089 DOI: 10.1038/s41467-021-25260-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 07/27/2021] [Indexed: 12/25/2022] Open
Abstract
Inactivating mutations in SMARCA4 and concurrent epigenetic silencing of SMARCA2 characterize subsets of ovarian and lung cancers. Concomitant loss of these key subunits of SWI/SNF chromatin remodeling complexes in both cancers is associated with chemotherapy resistance and poor prognosis. Here, we discover that SMARCA4/2 loss inhibits chemotherapy-induced apoptosis through disrupting intracellular organelle calcium ion (Ca2+) release in these cancers. By restricting chromatin accessibility to ITPR3, encoding Ca2+ channel IP3R3, SMARCA4/2 deficiency causes reduced IP3R3 expression leading to impaired Ca2+ transfer from the endoplasmic reticulum to mitochondria required for apoptosis induction. Reactivation of SMARCA2 by a histone deacetylase inhibitor rescues IP3R3 expression and enhances cisplatin response in SMARCA4/2-deficient cancer cells both in vitro and in vivo. Our findings elucidate the contribution of SMARCA4/2 to Ca2+-dependent apoptosis induction, which may be exploited to enhance chemotherapy response in SMARCA4/2-deficient cancers.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Medical Genetics, McGill University Health Centre, and Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Jordan L Morris
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Fraser Johnson
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Brian Meehan
- Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal Children's Hospital, McGill University, Montreal, QC, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Amber Yasmeen
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Tunde Golenar
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Mackenzie Coatham
- Department of Oncology, Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Anie Monast
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Virginie Pilon
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | | | - Sungmi Jung
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Anne V Gonzalez
- Department of Medicine, Division of Respiratory Medicine, McGill University Health Centre, Montreal Chest Institute, Montreal, QC, Canada
| | | | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Lynne-Marie Postovit
- Department of Oncology, Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Jonathan Spicer
- Department of Surgery, McGill University Health Center, Montreal, QC, Canada
| | - Walter H Gotlieb
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Marie-Christine Guiot
- Department of Pathology, Montreal Neurological Hospital/Institute, McGill University Health Centre, Montreal, QC, Canada
| | - Janusz Rak
- Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal Children's Hospital, McGill University, Montreal, QC, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - William Lockwood
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Medical Genetics, McGill University Health Centre, and Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada.
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62
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The BAF chromatin remodeling complexes: structure, function, and synthetic lethalities. Biochem Soc Trans 2021; 49:1489-1503. [PMID: 34431497 DOI: 10.1042/bst20190960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
Abstract
BAF complexes are multi-subunit chromatin remodelers, which have a fundamental role in genomic regulation. Large-scale sequencing efforts have revealed frequent BAF complex mutations in many human diseases, particularly in cancer and neurological disorders. These findings not only underscore the importance of the BAF chromatin remodelers in cellular physiological processes, but urge a more detailed understanding of their structure and molecular action to enable the development of targeted therapeutic approaches for diseases with BAF complex alterations. Here, we review recent progress in understanding the composition, assembly, structure, and function of BAF complexes, and the consequences of their disease-associated mutations. Furthermore, we highlight intra-complex subunit dependencies and synthetic lethal interactions, which have emerged as promising treatment modalities for BAF-related diseases.
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63
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Wang G, Wu M, Durham AC, Mason NJ, Roth DB. Canine Oncopanel: A capture-based, NGS platform for evaluating the mutational landscape and detecting putative driver mutations in canine cancers. Vet Comp Oncol 2021; 20:91-101. [PMID: 34286913 DOI: 10.1111/vco.12746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022]
Abstract
Canine cancer, a significant cause of mortality in domestic dogs, is a powerful comparative model for human cancers. Revealing genetic alterations driving the oncogenesis of canine cancers holds great potential to deepen our understanding of the cancer biology, guide therapeutic development, and improve cancer management in both dogs and people. Next generation sequencing (NGS) based-diagnostic panels have been routinely used in human oncology for the identification of clinically-actionable mutations, enabling tailored treatments based on the individual's unique mutation profiles. Here, we report the development of a comprehensive canine cancer gene panel, the Canine Oncopanel, using a hybridization capture-based targeted NGS method. The Canine Oncopanel allows deep sequencing of 283 cancer genes and the detection of somatic mutations within these genes. Vigorous optimization was performed to achieve robust, high-standard performance using metrics of similar cancer panels in human oncology as benchmarks. Validation of the Canine Oncopanel on reference tumour samples with known mutations demonstrated that it can detect variants previously identified by alternative methods, with high accuracy and sensitivity. Putative drivers were detected in over 90% of clinical samples, showing high sensitivity. The Canine Oncopanel is suitable to map mutation profiles and identify putative driver mutations across common and rare cancer types in dogs. The data generated by the Canine Oncopanel presents a rich resource of putative oncogenic driver mutations and potential clinically relevant markers, paving the way for personalized diagnostics and precision medicine in canine oncology.
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Affiliation(s)
- Guannan Wang
- Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ming Wu
- Service and Support, Illumina, San Diego, California, USA
| | - Amy C Durham
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicola J Mason
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David B Roth
- Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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64
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Romero OA, Vilarrubi A, Alburquerque-Bejar JJ, Gomez A, Andrades A, Trastulli D, Pros E, Setien F, Verdura S, Farré L, Martín-Tejera JF, Llabata P, Oaknin A, Saigi M, Piulats JM, Matias-Guiu X, Medina PP, Vidal A, Villanueva A, Sanchez-Cespedes M. SMARCA4 deficient tumours are vulnerable to KDM6A/UTX and KDM6B/JMJD3 blockade. Nat Commun 2021; 12:4319. [PMID: 34262032 PMCID: PMC8280185 DOI: 10.1038/s41467-021-24618-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
Despite the genetic inactivation of SMARCA4, a core component of the SWI/SNF-complex commonly found in cancer, there are no therapies that effectively target SMARCA4-deficient tumours. Here, we show that, unlike the cells with activated MYC oncogene, cells with SMARCA4 inactivation are refractory to the histone deacetylase inhibitor, SAHA, leading to the aberrant accumulation of H3K27me3. SMARCA4-mutant cells also show an impaired transactivation and significantly reduced levels of the histone demethylases KDM6A/UTX and KDM6B/JMJD3, and a strong dependency on these histone demethylases, so that its inhibition compromises cell viability. Administering the KDM6 inhibitor GSK-J4 to mice orthotopically implanted with SMARCA4-mutant lung cancer cells or primary small cell carcinoma of the ovary, hypercalcaemic type (SCCOHT), had strong anti-tumour effects. In this work we highlight the vulnerability of KDM6 inhibitors as a characteristic that could be exploited for treating SMARCA4-mutant cancer patients. SMARCA4 is commonly inactivated in lung and ovarian cancers. Here the authors show that SMARCA4-deficient tumours have significantly reduced levels of the histone demethylases KDM6s and a strong dependency on these demethylases for tumour growth, so that they are vulnerable to KDM6s inhibition.
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Affiliation(s)
- Octavio A Romero
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.
| | - Andrea Vilarrubi
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Juan J Alburquerque-Bejar
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Antonio Gomez
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Alvaro Andrades
- Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain.,GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Deborah Trastulli
- Genes and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute-IDIBELL Barcelona, Barcelona, Spain
| | - Eva Pros
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Fernando Setien
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Sara Verdura
- Genes and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute-IDIBELL Barcelona, Barcelona, Spain
| | - Lourdes Farré
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Juan F Martín-Tejera
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Paula Llabata
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Ana Oaknin
- Department of Medical Oncology, Vall d'Hebrón Hospital, Barcelona, Spain
| | - Maria Saigi
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.,Department of Medical Oncology, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Josep M Piulats
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, CIBERONC, L'Hospitalet del Llobregat, Barcelona, Spain
| | - Pedro P Medina
- Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain.,GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - August Vidal
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, CIBERONC, L'Hospitalet del Llobregat, Barcelona, Spain.,Xenopat S.L., Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain.,Xenopat S.L., Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - Montse Sanchez-Cespedes
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.
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65
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What Is New in Biomarker Testing at Diagnosis of Advanced Non-Squamous Non-Small Cell Lung Carcinoma? Implications for Cytology and Liquid Biopsy. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The discovery and clinical validation of biomarkers predictive of the response of non-squamous non-small-cell lung carcinomas (NS-NSCLC) to therapeutic strategies continue to provide new data. The evaluation of novel treatments is based on molecular analyses aimed at determining their efficacy. These tests are increasing in number, but the tissue specimens are smaller and smaller and/or can have few tumor cells. Indeed, in addition to tissue samples, complementary cytological and/or blood samples can also give access to these biomarkers. To date, it is recommended and necessary to look for the status of five genomic molecular biomarkers (EGFR, ALK, ROS1, BRAFV600, NTRK) and of a protein biomarker (PD-L1). However, the short- and more or less long-term emergence of new targeted treatments of genomic alterations on RET and MET, but also on others’ genomic alteration, notably on KRAS, HER2, NRG1, SMARCA4, and NUT, have made cellular and blood samples essential for molecular testing. The aim of this review is to present the interest in using cytological and/or liquid biopsies as complementary biological material, or as an alternative to tissue specimens, for detection at diagnosis of new predictive biomarkers of NS-NSCLC.
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66
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Nambirajan A, Jain D. Recent updates in thoracic SMARCA4-deficient undifferentiated tumor. Semin Diagn Pathol 2021; 38:83-89. [PMID: 34147303 DOI: 10.1053/j.semdp.2021.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022]
Abstract
Germline inactivating mutations in SMARCA4 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4) gene encoding for BRG1 (Brahma related gene-1) are the molecular drivers in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) and in malignant rhabdoid tumors (MRT) that occur in the context of rhabdoid tumor predisposition syndrome-type 2. Somatic SMARCA4 mutations and/or loss of BRG1 have been identified in a variety of adult-onset epithelial and mesenchymal neoplasms. Among thoracic tumors, these include subsets of smoking-related non-small cell lung carcinoma (NSCLC) and a relatively rare, newly recognised tumor entity: thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4-UT). Less than 100 cases of SMARCA4-UT have been reported to date. They present as large compressive and infiltrative mediastinal, lung and/or pleural masses in middle-aged male smokers. They are undifferentiated tumors composed of sheets of small/epithelioid and/or rhabdoid tumor cells variably expressing epithelial markers and consistently showing loss of BRG1 and the closely related protein, Brahma (BRM). Frequent expression of stem cell markers (SOX2, CD34, SALL4) is noted. Despite gene expression profiles similar to MRTs and SCCOHT, they show striking genomic overlap with SMARCA4-mutant NSCLC with frequent TP53, STK11, KEAP1, and KRAS mutations, high tumor mutation burden (TMB), and presence of smoking related molecular signatures in tumor cells. SMARCA4-UT show uniformly poor survival and are irresponsive to conventional therapies. Immunotherapy responses are variable but promising, although PDL1 expression appears to be of poor predictive value. Drugs exploiting genetic and epigenetic mechanisms of SMARCA4 antagonism hold promise for future targeted therapies.
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Affiliation(s)
- Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India.
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67
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Abstract
The epigenetic landscape, which in part includes DNA methylation, chromatin organization, histone modifications, and noncoding RNA regulation, greatly contributes to the heterogeneity that makes developing effective therapies for lung cancer challenging. This review will provide an overview of the epigenetic alterations that have been implicated in all aspects of cancer pathogenesis and progression as well as summarize clinical applications for targeting epigenetics in the treatment of lung cancer.
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Affiliation(s)
- Yvonne L Chao
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Chad V Pecot
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina, Chapel Hill, North Carolina 27514, USA
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Wanior M, Krämer A, Knapp S, Joerger AC. Exploiting vulnerabilities of SWI/SNF chromatin remodelling complexes for cancer therapy. Oncogene 2021; 40:3637-3654. [PMID: 33941852 PMCID: PMC8154588 DOI: 10.1038/s41388-021-01781-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 02/08/2023]
Abstract
Multi-subunit ATPase-dependent chromatin remodelling complexes SWI/SNF (switch/sucrose non-fermentable) are fundamental epigenetic regulators of gene transcription. Functional genomic studies revealed a remarkable mutation prevalence of SWI/SNF-encoding genes in 20-25% of all human cancers, frequently driving oncogenic programmes. Some SWI/SNF-mutant cancers are hypersensitive to perturbations in other SWI/SNF subunits, regulatory proteins and distinct biological pathways, often resulting in sustained anticancer effects and synthetic lethal interactions. Exploiting these vulnerabilities is a promising therapeutic strategy. Here, we review the importance of SWI/SNF chromatin remodellers in gene regulation as well as mechanisms leading to assembly defects and their role in cancer development. We will focus in particular on emerging strategies for the targeted therapy of SWI/SNF-deficient cancers using chemical probes, including proteolysis targeting chimeras, to induce synthetic lethality.
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Affiliation(s)
- Marek Wanior
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany.
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany.
- German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main, Germany.
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany.
- German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main, Germany.
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69
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Anžič N, Krasniqi F, Eberhardt AL, Tzankov A, Haslbauer JD. Ipilimumab and Pembrolizumab Mixed Response in a 41-Year-Old Patient with SMARCA4-Deficient Thoracic Sarcoma: An Interdisciplinary Case Study. Case Rep Oncol 2021; 14:706-715. [PMID: 34177520 PMCID: PMC8215992 DOI: 10.1159/000515416] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
SMARCA4-deficient thoracic sarcoma is a newly described entity of thoracic sarcomas with a poor prognosis, defined by poorly differentiated epithelioid to rhabdoid histomorphology and SMARCA4 gene inactivation. We present a case of a SMARCA4-deficient thoracic sarcoma in a 41-year-old male with a smoking history who presented with an upper anterior mediastinal mass, after seeking medical evaluation for increasing thoracic pain, odynophagia, and dizziness. The biopsy confirmed a large cell tumor with an epithelioid to rhabdoid histomorphology, positive for EMA, CD99, vimentin, TLE1, INI1, PAS-positive cytoplasmic granules, and PD-L1 (100% of tumor cells). High TMB and HRD scores were displayed in the tumor. The histology and immunophenotype of the mass were in line with the diagnosis of SMARCA4-deficient thoracic sarcoma. In the course of his treatment, the patient showcased a partial response to pembrolizumab and the combination of pembrolizumab and ipilimumab. This case report highlights the importance of recognizing SMARCA4-deficient thoracic sarcoma as an individual entity and supports the importance of checkpoint inhibition therapy for SMARCA4-deficient thoracic sarcomas, particularly in cases with a high TMB and PD-L1 expression.
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Affiliation(s)
- Nina Anžič
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Fatime Krasniqi
- Centre of Oncology, University Hospital Basel, Basel, Switzerland
| | | | - Alexandar Tzankov
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
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70
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Duan W, Wang K, Duan Y, Chen X, Chu X, Hu P, Xiong B. Combined Analysis of RNA Sequence and Microarray Data Reveals a Competing Endogenous RNA Network as Novel Prognostic Markers in Malignant Pleural Mesothelioma. Front Oncol 2021; 11:615234. [PMID: 33968720 PMCID: PMC8104912 DOI: 10.3389/fonc.2021.615234] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a highly aggressive cancer with short survival time. Unbalanced competing endogenous RNAs (ceRNAs) have been shown to participate in the tumor pathogenesis and served as biomarkers for the clinical prognosis. However, the comprehensive analyses of the ceRNA network in the prognosis of MPM are still rarely reported. In this study, we obtained the transcriptome data of the MPM and the normal samples from TCGA, EGA, and GEO databases and identified the differentially expressed (DE) mRNAs, lncRNAs, and miRNAs. The functions of the prognostic genes and the overlapped DEmRNAs were further annotated by the multiple enrichment analyses. Then, the targeting relationships among lncRNA–miRNA and miRNA–mRNA were predicted and calculated, and a prognostic ceRNA regulatory network was established. We included the prognostic 73 mRNAs and 13 miRNAs and 26 lncRNAs into the ceRNA network. Moreover, 33 mRNAs, three miRNAs, and seven lncRNAs were finally associated with prognosis, and a model including seven mRNAs, two lincRNAs, and some clinical factors was finally established and validated by two independent cohorts, where CDK6 and SGMS1-AS1 were significant to be independent prognostic factors. In addition, the identified co-expressed modules associated with the prognosis were overrepresented in the ceRNA network. Multiple enrichment analyses showed the important roles of the extracellular matrix components and cell division dysfunction in the invasion of MPM potentially. In summary, the prognostic ceRNA network of MPM was established and analyzed for the first time and these findings shed light on the function of ceRNAs and revealed the potential prognostic and therapeutic biomarkers of MPM.
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Affiliation(s)
- Weicheng Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yijie Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiuyi Chen
- Key Laboratory of Environment and Health (HUST), Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xufeng Chu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Hu
- Key Laboratory of Environment and Health (HUST), Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Xiong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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71
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Duan H, Gao W, Wang L, Cao F, Teng L. Undifferentiated colonic neoplasm with SMARCA4 germline gene mutation and loss of SMARCA4 protein expression: a case report and literature review. Diagn Pathol 2021; 16:30. [PMID: 33836796 PMCID: PMC8033741 DOI: 10.1186/s13000-021-01091-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/29/2021] [Indexed: 12/29/2022] Open
Abstract
Background Nonsense mutation or inactivation of SMARCA4 (BRG1) is associated with a monomorphic undifferentiated histological appearance in tumors at different sites. The association between SMARCA4 alteration and undifferentiated colonic carcinoma needs to be further elucidated. Methods A 61-year-old male patient presented to the hospital with intermittent epigastric pain in the right upper abdomen and abdominal distension. The enhanced computed tomography detected a mass in the hepatic flexure of the colon and multiple liver metastases. Results The right hemicolectomy contained a 4.5-cm undifferentiated malignancy with cells arranged in sheets, abundant necrosis, and areas showing rhabdoid morphology. The immunohistochemistry result showed that these tumor cells were focally positive for cytokeratin (CK), CK8, and CK18; however, diffusely positive for vimentin, P53, Fli-1, and SALL-4. Notably, tumor cells showed a heterogeneous loss of SMARCA4 expression pattern and intact SMARCB1 expression. Next-generation sequencing showed a germline SMARCA4 c.3277C>T(p.R1093*)mutation, somatic APC mutation, and no abnormal SMARCB1 gene. The tumor exhibited microsatellite stability, negative PD-L1 expression, and few infiltrating CD8 + T cells. The patient died a month later after surgery. Conclusions We presented a rare case of undifferentiated colonic neoplasm with loss of SMARCA4 protein expression and germline SMARCA4 mutation. Moreover, the role of SMARCA4 alterations in tumor diagnosis and treatment was also summarized. Supplementary Information The online version contains supplementary material available at 10.1186/s13000-021-01091-6.
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Affiliation(s)
- Huanli Duan
- Department of Pathology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, China
| | - Wei Gao
- Department of Pathology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, China
| | - Leiming Wang
- Department of Pathology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, China
| | - Feng Cao
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, China
| | - Lianghong Teng
- Department of Pathology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, China.
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72
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Agaimy A. Moving from "single gene" concept to "functionally homologous multigene complex": The SWI/SNF paradigm. Semin Diagn Pathol 2021; 38:165-166. [PMID: 33712319 DOI: 10.1053/j.semdp.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany.
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73
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Agaimy A, Bishop JA. SWI/SNF-deficient head and neck neoplasms: An overview. Semin Diagn Pathol 2021; 38:175-182. [PMID: 33663878 DOI: 10.1053/j.semdp.2021.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/11/2022]
Abstract
With wide-spread use of next generation sequencing tools in surgical pathology, a variety of neoplasms have been increasingly recognized to be associated with specific recurrent defining genetic abnormalities. This has led to recognition of new genetically defined entities and refinements of preexisting heterogeneous neoplastic categories. Among these, neoplasms associated with inactivating mutations involving different subunits of the SWI/SNF chromatin remodeling complex have received special attention. In the head and neck area, SMARCB1 (INI1) and SMARCA4 (BRG1) are the main two SWI/SNF components responsible for several recently described highly aggressive undifferentiated malignancies with predilection for the soft tissue of the neck (SMARCB1-deficient malignant rhabdoid tumors in children and rare epithelioid sarcoma cases in adults) and the sinonasal tract (SMARCB1-deficient sinonasal carcinoma including a small subset of adenocarcinomas, SMARCA4-deficient sinonasal undifferentiated carcinoma and SMARCA4-deficient sinonasal teratocarcinosarcoma). Molecular studies confirmed paucity of additional genetic abnormalities in these diseases underlining the central role of SWI/SNF deficiency as the primary and frequently sole genetic driver of these lethal diseases. Initiation of clinical trials using drugs that target the SWI/SNF collapse encourages recognition and correct classification of these morphologically frequently overlapping malignancies and underpins the role of SWI/SNF immunohistochemistry as emerging powerful adjunct tool in surgical pathology of the head and neck.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany.
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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74
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Stodolna A, He M, Vasipalli M, Kingsbury Z, Becq J, Stockton JD, Dilworth MP, James J, Sillo T, Blakeway D, Ward ST, Ismail T, Ross MT, Beggs AD. Clinical-grade whole-genome sequencing and 3' transcriptome analysis of colorectal cancer patients. Genome Med 2021; 13:33. [PMID: 33632293 PMCID: PMC7908713 DOI: 10.1186/s13073-021-00852-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/11/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Colorectal cancer presents a difficult treatment paradigm, with over 40% of patients presenting at diagnosis with metastatic disease. We hypothesised that cWGS coupled with 3' transcriptome analysis would give new insights into colorectal cancer. METHODS Patients underwent PCR-free whole-genome sequencing and alignment and variant calling using a standardised pipeline to output SNVs, indels, SVs and CNAs. Additional insights into the mutational signatures and tumour biology were gained by the use of 3' RNA-seq. RESULTS Fifty-four patients were studied in total. Driver analysis identified the Wnt pathway gene APC as the only consistently mutated driver in colorectal cancer. Alterations in the PI3K/mTOR pathways were seen as previously observed in CRC. Multiple private CNAs, SVs and gene fusions were unique to individual tumours. Approximately 30% of patients had a tumour mutational burden of > 10 mutations/Mb of DNA, suggesting suitability for immunotherapy. CONCLUSIONS Clinical whole-genome sequencing offers a potential avenue for the identification of private genomic variation that may confer sensitivity to targeted agents and offer patients new options for targeted therapies.
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Affiliation(s)
- Agata Stodolna
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Miao He
- Illumina Cambridge, Granta Park, Cambridge, UK
| | | | | | | | - Joanne D Stockton
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Mark P Dilworth
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jonathan James
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Toju Sillo
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Daniel Blakeway
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Stephen T Ward
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Tariq Ismail
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Mark T Ross
- Illumina Cambridge, Granta Park, Cambridge, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, Vincent Drive, Birmingham, B15 2TT, UK.
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75
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Zengin T, Önal-Süzek T. Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. J Pers Med 2021; 11:154. [PMID: 33672117 PMCID: PMC7926392 DOI: 10.3390/jpm11020154] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer type and responsible for the highest number of cancer deaths worldwide. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are subtypes of non-small-cell lung cancer which has the highest frequency of lung cancer cases. We aimed to analyze genomic and transcriptomic variations including simple nucleotide variations (SNVs), copy number variations (CNVs) and differential expressed genes (DEGs) in order to find key genes and pathways for diagnostic and prognostic prediction for lung adenocarcinoma and lung squamous cell carcinoma. We performed a univariate Cox model and then lasso-regularized Cox model with leave-one-out cross-validation using The Cancer Genome Atlas (TCGA) gene expression data in tumor samples. We generated 35- and 33-gene signatures for prognostic risk prediction based on the overall survival time of the patients with LUAD and LUSC, respectively. When we clustered patients into high- and low-risk groups, the survival analysis showed highly significant results with high prediction power for both training and test datasets. Then, we characterized the differences including significant SNVs, CNVs, DEGs, active subnetworks, and the pathways. We described the results for the risk groups and cancer subtypes separately to identify specific genomic alterations between both high-risk groups and cancer subtypes. Both LUAD and LUSC high-risk groups have more downregulated immune pathways and upregulated metabolic pathways. On the other hand, low-risk groups have both up- and downregulated genes on cancer-related pathways. Both LUAD and LUSC have important gene alterations such as CDKN2A and CDKN2B deletions with different frequencies. SOX2 amplification occurs in LUSC and PSMD4 amplification in LUAD. EGFR and KRAS mutations are mutually exclusive in LUAD samples. EGFR, MGA, SMARCA4, ATM, RBM10, and KDM5C genes are mutated only in LUAD but not in LUSC. CDKN2A, PTEN, and HRAS genes are mutated only in LUSC samples. The low-risk groups of both LUAD and LUSC tend to have a higher number of SNVs, CNVs, and DEGs. The signature genes and altered genes have the potential to be used as diagnostic and prognostic biomarkers for personalized oncology.
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Affiliation(s)
- Talip Zengin
- Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey;
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
| | - Tuğba Önal-Süzek
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
- Department of Computer Engineering, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
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76
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Chong PSY, Chooi JY, Lim JSL, Toh SHM, Tan TZ, Chng WJ. SMARCA2 Is a Novel Interactor of NSD2 and Regulates Prometastatic PTP4A3 through Chromatin Remodeling in t(4;14) Multiple Myeloma. Cancer Res 2021; 81:2332-2344. [PMID: 33602783 DOI: 10.1158/0008-5472.can-20-2946] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
NSD2 is the primary oncogenic driver in t(4;14) multiple myeloma. Using SILAC-based mass spectrometry, we demonstrate a novel role of NSD2 in chromatin remodeling through its interaction with the SWI/SNF ATPase subunit SMARCA2. SMARCA2 was primarily expressed in t(4;14) myeloma cells, and its interaction with NSD2 was noncanonical and independent of the SWI/SNF complex. RNA sequencing identified PTP4A3 as a downstream target of NSD2 and mapped NSD2-SMARCA2 complex on PTP4A3 promoter. This led to a focal increase in the permissive H3K36me2 mark and transcriptional activation of PTP4A3. High levels of PTP4A3 maintained MYC expression and correlated with a 54-gene MYC signature in t(4;14) multiple myeloma. Importantly, this mechanism was druggable by targeting the bromodomain of SMARCA2 using the specific BET inhibitor PFI-3, leading to the displacement of NSD2 from PTP4A3 promoter and inhibiting t(4;14) myeloma cell viability. In vivo, treatment with PFI-3 reduced the growth of t(4;14) xenograft tumors. Together, our study reveals an interplay between histone-modifying enzymes and chromatin remodelers in the regulation of myeloma-specific genes that can be clinically intervened. SIGNIFICANCE: This study uncovers a novel, SWI/SNF-independent interaction between SMARCA2 and NSD2 that facilitates chromatin remodeling and transcriptional regulation of oncogenes in t(4;14) multiple myeloma, revealing a therapeutic vulnerability targetable by BET inhibition.
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Affiliation(s)
- Phyllis S Y Chong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Jing Yuan Chooi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Julia S L Lim
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sabrina Hui Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Heamatology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore
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77
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Tsuda M, Fukuda A, Kawai M, Araki O, Seno H. The role of the SWI/SNF chromatin remodeling complex in pancreatic ductal adenocarcinoma. Cancer Sci 2021; 112:490-497. [PMID: 33301642 PMCID: PMC7894000 DOI: 10.1111/cas.14768] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes are a group of epigenetic regulators that can alter the assembly of nucleosomes and regulate the accessibility of transcription factors to DNA in order to modulate gene expression. One of these complexes, the SWI/SNF chromatin remodeling complex is mutated in more than 20% of human cancers. We have investigated the roles of the SWI/SNF complex in pancreatic ductal adenocarcinoma (PDA), which is the most lethal type of cancer. Here, we reviewed the recent literature regarding the role of the SWI/SNF complex in pancreatic tumorigenesis and current knowledge about therapeutic strategies targeting the SWI/SNF complex in PDA. The subunits of the SWI/SNF complex are mutated in 14% of human PDA. Recent studies have shown that they have context-dependent oncogenic or tumor-suppressive roles in pancreatic carcinogenesis. To target its tumor-suppressive properties, synthetic lethal strategies have recently been developed. In addition, their oncogenic properties could be novel therapeutic targets. The SWI/SNF subunits are potential therapeutic targets for PDA, and further understanding of the precise role of the SWI/SNF complex subunits in PDA is required for further development of novel strategies targeting SWI/SNF subunits against PDA.
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Affiliation(s)
- Motoyuki Tsuda
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
- Department of Gastroenterology and HepatologyKindai University Faculty of MedicineOsaka‐sayama CityJapan
| | - Akihisa Fukuda
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
| | - Munenori Kawai
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
| | - Osamu Araki
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
| | - Hiroshi Seno
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
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78
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Intrinsic and acquired resistance to CDK4/6 inhibitors and potential overcoming strategies. Acta Pharmacol Sin 2021; 42:171-178. [PMID: 32504067 DOI: 10.1038/s41401-020-0416-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Abnormal activation of the cyclin-dependent kinases (CDKs), which result in aberrant cell proliferation, is one of the inherent characteristics of tumor. Thus targeting the activity of CDKs represents a promising tumor therapeutic strategy. Currently, the specific inhibitors that target CDK4 and CDK6 have been approved for the treatment of estrogen receptor positive, human epidermal growth factor receptor 2 negative (ER+ HER2-) breast cancer in combination with endocrine therapy; other combination strategies are being tested in a number of clinical trials. However, the acquired resistance to CDK4/6 inhibitors has emerged. As the cell cycle is orchestrated by a series of biological events, the alterations of other molecular events that regulate the cell cycle progression may be involved in intrinsic resistance to CDK4/6 inhibitors. In this review we mainly discuss the mechanisms underlying intrinsic resistance and acquired resistance to CDK4/6 inhibitors as well as combination strategies with other signal pathway inhibitors being tested in clinical and pre-clinical studies, to extend the use of CDK4/6 inhibitors in tumor treatment.
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79
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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80
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Sesboue C, Le Loarer F. SWI/SNF-deficient thoraco-pulmonary neoplasms. Semin Diagn Pathol 2021; 38:183-194. [PMID: 33451916 DOI: 10.1053/j.semdp.2020.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022]
Abstract
The SWI/SNF complexes are major regulators of gene expression and their alterations occur in a large array of cancers both of epithelial and mesenchymal lineages. Malignant rhabdoid tumors were the first malignancies linked to deregulation of these complexes with the involvement of SMARCB1 in their development but genetic alterations affect all subunits in other malignancies. In the chest and lung regions, SMARCA4 (BRG1) is the most frequently altered subunit and is involved in the pathogenesis of two subtypes of tumors, including bona fide carcinomas (SMARCA4-deficient non-small cell lung cancers) but also undifferentiated tumors that harbor an undifferentiated phenotype close to those of malignant rhabdoid tumors (SMARCA4-undifferentiated tumors). Although their histogenesis is yet to be fully understood, these tumors are associated with distinct clinical and pathological features even though some overlapping features have been reported in rare cases. SMARCA4 deficiency is easily asserted by immunohistochemistry that show the loss of nuclear expression of the protein in the nuclei of tumor cells. These tumors are commonly associated with high-grade cytological features, rhabdoid cytomorphology, solid architecture and extensive necrosis. The typical immunohistochemical signature of SMARCA4-UT combines co-inactivation of SMARCA2 (BRM) and the overexpression of SOX2 and SALL4. No specific therapeutic strategies have been so far developed for SMARCA4-deficient neoplasms. SMARCB1 subunit is involved in the development of several SMARCB1-deficient sarcomas on top of malignant rhabdoid tumors that may develop in the thorax. Malignant rhabdoid tumors affect mostly children of less than 5y. The differential diagnosis includes epithelioid sarcomas, malignant myoepithelial tumors or myoepithelial carcinomas, extra-skeletal myxoid chondrosarcomas and synovial sarcomas.
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Affiliation(s)
- Come Sesboue
- University of Bordeaux, Talence, France; Cancer center of Bordeaux, Bordeaux, France
| | - Francois Le Loarer
- University of Bordeaux, Talence, France; Cancer center of Bordeaux, Bordeaux, France; INSERM U1218, Siric Brio, Cancer center of Bordeaux, Bordeaux, France.
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81
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The genomic and immunologic profiles of pure pulmonary sarcomatoid carcinoma in Chinese patients. Lung Cancer 2021; 153:66-72. [PMID: 33454519 DOI: 10.1016/j.lungcan.2021.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/11/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE The distribution of genetic mutations differs between pure pulmonary sarcomatoid carcinoma (PSC) and biphasic PSC; however, most of the enrolled cases in previous studies are biphasic PSC. The current study aimed to investigate the genomic and immunologic profiles of pure PSC in the Chinese population. MATERIALS AND METHODS Next-generation sequencing analysis of a panel of 1021 genes was performed on surgical specimens of 58 pure PSCs. The tumor mutational burden (TMB) was calculated from 0.69 megabases (Mbs) of sequenced DNA. PD-L1 expression was evaluated by immunohistochemistry. Microsatellite instability (MSI) was evaluated by fluorescence-labeled microsatellite marker polymerase chain reaction followed by capillary electrophoresis fragment size analysis. RESULTS The top mutational genes of pure PSC were TP53 (74 %, 43/58), KRAS (24 %, 14/58), SMARCA4 (14 %, 8/58), MET (12 %, 7/58), EGFR (10 %, 6/58), MLL4 (10 %, 6/58), NF1 (10 %, 6/58), NOTCH4 (10 %, 6/58), and TERT (10 %, 6/58). The median TMB was 8.6 mutations/Mb; 37.9 % of cases (22/58) had a TMB > 10 mutations/Mb and 12.1 % of cases (7/58) had a TMB > 20 mutations/Mb. The median TMB was higher in TP53-mutant tumors than in wild-type tumors (10.1 versus 7.2 mutations/Mb, p = 0.019). Thirty-five patients had microsatellite-stable pure PSC, and four patients carried MSI-H tumors. The MSI status was independent of MET exon 14 status. Twenty-six patients (45 %) had PD-L1-positive tumors (≥1%) and 14 (24 %) had high PD-L1 expression (≥50 %). CONCLUSION In our cohort, 45 % of patients with pure PSC harbored at least one actionable alteration. More importantly, more than 60 % of patients (65.5 %, 38/58) had either MSI-H, PD-L1-positive, or high-TMB tumors, and these might derive survival benefits from immune checkpoint inhibitors.
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82
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Yang Y, Chen X, Ma C. Insulin receptor is implicated in triple-negative breast cancer by decreasing cell mobility. J Biomed Res 2021; 35:189-196. [PMID: 33911052 PMCID: PMC8193710 DOI: 10.7555/jbr.34.20200082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has a poor prognosis and typically earlier onset of metastasis in comparison with other breast cancer subtypes. It has been reported that insulin receptor (INSR) is downregulated in TNBC, however, its clinical significance and functions in TNBC remain to be elucidated. In this study, we found that INSR expression was significantly downregulated in TNBC, and overexpression of INSR suppressed cell migration and invasion in TNBC. In addition, the survival rate of breast cancer patients with low INSR expression was lower than that of patients with high INSR expression. INSR expression was significantly correlated with lymph node metastasis, clinical tumor stages, ER status, PR status, and the proliferation index Ki-67 expression. In summary, our study suggests that INSR may serve as a biomarker for breast cancer prognosis and it may be a potential target for TNBC treatment.
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Affiliation(s)
- Ying Yang
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiang Chen
- Department of General Surgery, the Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu 214200, China
| | - Changyan Ma
- Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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83
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Huang Z, Xu Y, Wan M, Zeng X, Wu J. miR-340: A multifunctional role in human malignant diseases. Int J Biol Sci 2021; 17:236-246. [PMID: 33390846 PMCID: PMC7757049 DOI: 10.7150/ijbs.51123] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/09/2020] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of short non-coding RNAs of approximately 22 nucleotides in length, which function by binding to the 3' UTR sequences of their target mRNAs. It has been reported that dysregulated miRNAs play pivotal roles in numerous diseases, including cancers, such as gastric, breast, colorectal, ovarian, and other cancers. Recent research efforts have been devoted to translating these basic discoveries into clinical applications that could improve the therapeutic outcome in patients with cancer. Early studies have shown that miR-340 may act either as an oncogene or a tumor suppressor by targeting genes related to proliferation, apoptosis, and metastasis, as well as those associated with diagnosis, treatment, chemoresistance, and prognosis. miR-340 has been shown to have a role in other diseases, such as autoimmune diseases, acute stroke, and alcoholic steatohepatitis. Nevertheless, the roles of miR-340 in human malignancies are still unclear, and the associated mechanisms are complex, involving a variety of signaling pathways, such as Wnt/β-catenin and the JAK-STAT pathways. Herein, we review the crucial roles of miR-340 in human cancers through the analysis of the latest research studies, with the aim of clarifying miR-340 function in malignant disease diagnosis, treatment, and prognosis, and to propose further investigations.
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Affiliation(s)
- Zheng Huang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang, P.R. China
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yesha Xu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang, P.R. China
| | - Maoping Wan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang, P.R. China
| | - Xixi Zeng
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang, P.R. China
| | - Jianmin Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang, P.R. China
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84
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Orlando KA, Douglas AK, Abudu A, Wang Y, Tessier-Cloutier B, Su W, Peters A, Sherman LS, Moore R, Nguyen V, Negri GL, Colborne S, Morin GB, Kommoss F, Lang JD, Hendricks WP, Raupach EA, Pirrotte P, Huntsman DG, Trent JM, Parker JS, Raab JR, Weissman BE. Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism. eLife 2020; 9:59073. [PMID: 33355532 PMCID: PMC7813545 DOI: 10.7554/elife.59073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 reexpression. BRG1 reexpression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription-factor-binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant-negative AP-1 cell line, we found that both AP-1 DNA-binding activity and BRG1 reexpression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 reexpression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.
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Affiliation(s)
- Krystal Ann Orlando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Amber K Douglas
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Aierken Abudu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Weiping Su
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Alec Peters
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States.,Department Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Rayvon Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Vinh Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Gian Luca Negri
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Shane Colborne
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | - Jessica D Lang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - William Pd Hendricks
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Elizabeth A Raupach
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Jeffrey M Trent
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Jesse R Raab
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
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85
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Liu L, Ahmed T, Petty WJ, Grant S, Ruiz J, Lycan TW, Topaloglu U, Chou PC, Miller LD, Hawkins GA, Alexander-Miller MA, O'Neill SS, Powell BL, D'Agostino RB, Munden RF, Pasche B, Zhang W. SMARCA4 mutations in KRAS-mutant lung adenocarcinoma: a multi-cohort analysis. Mol Oncol 2020; 15:462-472. [PMID: 33107184 PMCID: PMC7858279 DOI: 10.1002/1878-0261.12831] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/11/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022] Open
Abstract
KRAS is a key oncogenic driver in lung adenocarcinoma (LUAD). Chromatin‐remodeling gene SMARCA4 is comutated with KRAS in LUAD; however, the impact of SMARCA4 mutations on clinical outcome has not been adequately established. This study sought to shed light on the clinical significance of SMARCA4 mutations in LUAD. The association of SMARCA4 mutations with survival outcomes was interrogated in four independent cohorts totaling 564 patients: KRAS‐mutant patients with LUAD who received nonimmunotherapy treatment from (a) The Cancer Genome Atlas (TCGA) and (b) the MSK‐IMPACT Clinical Sequencing (MSK‐CT) cohorts; and KRAS‐mutant patients with LUAD who received immune checkpoint inhibitor‐based immunotherapy treatment from (c) the MSK‐IMPACT (MSK‐IO) and (d) the Wake Forest Baptist Comprehensive Cancer Center (WFBCCC) immunotherapy cohorts. Of the patients receiving nonimmunotherapy treatment, in the TCGA cohort (n = 155), KRAS‐mutant patients harboring SMARCA4 mutations (KS) showed poorer clinical outcome [P = 6e‐04 for disease‐free survival (DFS) and 0.031 for overall survival (OS), respectively], compared to KRAS‐TP53 comutant (KP) and KRAS‐only mutant (K) patients; in the MSK‐CT cohort (n = 314), KS patients also exhibited shorter OS than KP (P = 0.03) or K (P = 0.022) patients. Of patients receiving immunotherapy, KS patients consistently exhibited the shortest progression‐free survival (PFS; P = 0.0091) in the MSK‐IO (n = 77), and the shortest PFS (P = 0.0026) and OS (P = 0.0014) in the WFBCCC (n = 18) cohorts, respectively. Therefore, mutations of SMARCA4 represent a genetic factor leading to adverse clinical outcome in lung adenocarcinoma treated by either nonimmunotherapy or immunotherapy.
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Affiliation(s)
- Liang Liu
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tamjeed Ahmed
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - William J Petty
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Stefan Grant
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jimmy Ruiz
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas W Lycan
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Umit Topaloglu
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ping-Chieh Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lance D Miller
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Stacey S O'Neill
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Pathology and Laboratory Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Bayard L Powell
- Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ralph B D'Agostino
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Reginald F Munden
- Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Boris Pasche
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Internal Medicine-Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
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86
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Howitt BE, Folpe AL. Update on SWI/SNF-related gynecologic mesenchymal neoplasms: SMARCA4-deficient uterine sarcoma and SMARCB1-deficient vulvar neoplasms. Genes Chromosomes Cancer 2020; 60:190-209. [PMID: 33252159 DOI: 10.1002/gcc.22922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 01/22/2023] Open
Abstract
Our knowledge regarding the role of genes encoding the chromatin remodeling switch/sucrose non-fermenting (SWI/SNF) complex in the initiation and progression of gynecologic malignancies continues to evolve. This review focuses on gynecologic tumors in which the sole or primary genetic alteration is in SMARCA4 or SMARCB1, two members of the SWI/SNF chromatin remodeling complex. In this review, we present a brief overview of the classical example of such tumors, ovarian small cell carcinoma of hypercalcemic type, and then a detailed review and update of SMARCB1-deficient and SMARCA4-deficient tumors of the uterus and vulva.
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Affiliation(s)
- Brooke E Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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87
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Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models. Cancers (Basel) 2020; 12:cancers12123712. [PMID: 33321963 PMCID: PMC7763689 DOI: 10.3390/cancers12123712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/29/2020] [Accepted: 12/08/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Mammalian SWI/SNF complexes regulate gene expression by reorganizing the way DNA is packaged into chromatin. SWI/SNF subunits are recurrently altered in tumors at multiple levels, including DNA mutations as well as alteration of the levels of RNA and protein. Cancer cell lines are often used to study SWI/SNF function, but their patterns of SWI/SNF alterations can be complex. Here, we present a comprehensive characterization of DNA mutations and RNA and protein expression of SWI/SNF members in 38 lung adenocarcinoma (LUAD) cell lines. We show that over 85% of our cell lines harbored at least one alteration in one SWI/SNF subunit. In addition, over 75% of our cell lines lacked expression of at least one SWI/SNF subunit at the protein level. Our catalog will help researchers choose an appropriate cell line model to study SWI/SNF function in LUAD. Abstract Mammalian SWI/SNF (SWitch/Sucrose Non-Fermentable) complexes are ATP-dependent chromatin remodelers whose subunits have emerged among the most frequently mutated genes in cancer. Studying SWI/SNF function in cancer cell line models has unveiled vulnerabilities in SWI/SNF-mutant tumors that can lead to the discovery of new therapeutic drugs. However, choosing an appropriate cancer cell line model for SWI/SNF functional studies can be challenging because SWI/SNF subunits are frequently altered in cancer by various mechanisms, including genetic alterations and post-transcriptional mechanisms. In this work, we combined genomic, transcriptomic, and proteomic approaches to study the mutational status and the expression levels of the SWI/SNF subunits in a panel of 38 lung adenocarcinoma (LUAD) cell lines. We found that the SWI/SNF complex was mutated in more than 76% of our LUAD cell lines and there was a high variability in the expression of the different SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the difficulties in defining altered and unaltered cell models for the SWI/SNF complex. These findings will assist researchers in choosing the most suitable cellular models for their studies of SWI/SNF to bring all of its potential to the development of novel therapeutic applications.
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88
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Abstract
Molecular analysis has reshaped the landscape of high grade sinonasal tumors by defining novel entities and identifying recurrent mutations in established tumor types. However, sinonasal teratocarcinosarcoma (TCS), a rare and aggressive tumor with intermixed teratomatous, carcinomatous, and sarcomatous elements, remains poorly understood. The multiphenotypic differentiation of TCS has engendered persistent controversy about its histogenesis and leads to diagnostic overlap with several other malignancies. In this study, we evaluated the molecular underpinnings of TCS to clarify its pathogenesis and diagnosis. We performed SMARCA4 immunohistochemistry (IHC) on 22 TCS and 153 other sinonasal tumors. We identified loss of SMARCA4 expression in 18 TCS (82%), including 15 (68%) with complete loss and 3 (14%) with partial loss. Although we also identified partial SMARCA4 loss in 1 of 8 SMARCB1-deficient sinonasal carcinomas (13%), SMARCA4 was intact in all other sinonasal carcinomas and neuroendocrine tumors. We then selected 3 TCS with complete SMARCA4 loss by IHC for a targeted next-generation sequencing panel that included 1425 cancer-related genes. We confirmed biallelic somatic inactivation of SMARCA4 without other known oncogenic mutations in these 3 cases. Overall, these findings suggest that SMARCA4 inactivation may be the dominant genetic event in TCS, expanding understanding of this gene's role in sinonasal tumorigenesis. They also raise the possibility that TCS is on a diagnostic spectrum with the newly described SMARCA4-deficient sinonasal carcinoma, blurring the lines between established and emerging sinonasal entities. In addition, SMARCA4 IHC may provide a useful adjunct for confirming a diagnosis of TCS in limited material.
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89
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Yang Y, Wang C, Wei N, Hong T, Sun Z, Xiao J, Yao J, Li Z, Liu T. Identification of prognostic chromatin-remodeling genes in clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:25614-25642. [PMID: 33232269 PMCID: PMC7803503 DOI: 10.18632/aging.104170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
The aim of this study was to investigate the effects of chromatin-remodeling genes on the prognosis of patients with clear cell renal cell carcinoma (ccRCC). In TCGA-KIRC patients, two subgroups based on 86 chromatin-remodeling genes were established. The random forest algorithm was used for feature selection to identify BPTF, SIN3A and CNOT1 as characterized chromatin remodelers in ccRCC with good prognostic value. YY1 was indicated to be a transcription factor of genes highly related to BPTF, SIN3A and CNOT1. Functional annotations indicated that BPTF, SIN3A, CNOT1 and YY1 are all involved in the ubiquitin-mediated proteolysis process and that high expression of any of the five associated E3 ubiquitin ligases found in the pathway suggests a good prognosis. Protein network analysis indicated that BPTF has a targeted regulatory effect on YY1. Another independent dataset from International Cancer Genome Consortium (ICGC) showed a strong consistency with results in TCGA. In conclusion, we demonstrate that BPTF, SIN3A and CNOT1 are novel prognostic factors that predict good survival in ccRCC. We predicted that the good prognostic value of chromatin-remodeling genes BPTF and SIN3A is related to the regulation of YY1 and that YY1 regulates E3 ubiquitin ligases for further degradation of oncoproteins in ccRCC.
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Affiliation(s)
- Yujing Yang
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Chengyuan Wang
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ningde Wei
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ting Hong
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zuyu Sun
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Jiawen Xiao
- Department of Medical Oncology, Shenyang Fifth People Hospital, Tiexi District, Shenyang 110001, P.R. China
| | - Jiaxi Yao
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zhi Li
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Tao Liu
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
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90
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Gupta M, Concepcion CP, Fahey CG, Keshishian H, Bhutkar A, Brainson CF, Sanchez-Rivera FJ, Pessina P, Kim JY, Simoneau A, Paschini M, Beytagh MC, Stanclift CR, Schenone M, Mani DR, Li C, Oh A, Li F, Hu H, Karatza A, Bronson RT, Shaw AT, Hata AN, Wong KK, Zou L, Carr SA, Jacks T, Kim CF. BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency. Cancer Res 2020; 80:3841-3854. [PMID: 32690724 PMCID: PMC7501156 DOI: 10.1158/0008-5472.can-20-1744] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/15/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022]
Abstract
Inactivation of SMARCA4/BRG1, the core ATPase subunit of mammalian SWI/SNF complexes, occurs at very high frequencies in non-small cell lung cancers (NSCLC). There are no targeted therapies for this subset of lung cancers, nor is it known how mutations in BRG1 contribute to lung cancer progression. Using a combination of gain- and loss-of-function approaches, we demonstrate that deletion of BRG1 in lung cancer leads to activation of replication stress responses. Single-molecule assessment of replication fork dynamics in BRG1-deficient cells revealed increased origin firing mediated by the prelicensing protein, CDC6. Quantitative mass spectrometry and coimmunoprecipitation assays showed that BRG1-containing SWI/SNF complexes interact with RPA complexes. Finally, BRG1-deficient lung cancers were sensitive to pharmacologic inhibition of ATR. These findings provide novel mechanistic insight into BRG1-mutant lung cancers and suggest that their dependency on ATR can be leveraged therapeutically and potentially expanded to BRG1-mutant cancers in other tissues. SIGNIFICANCE: These findings indicate that inhibition of ATR is a promising therapy for the 10% of non-small cell lung cancer patients harboring mutations in SMARCA4/BRG1. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/18/3841/F1.large.jpg.
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Affiliation(s)
- Manav Gupta
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences PhD Program, Harvard University, Boston, Massachusetts
| | - Carla P Concepcion
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Caroline G Fahey
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | | | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christine F Brainson
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | | | - Patrizia Pessina
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Y Kim
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antoine Simoneau
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Margherita Paschini
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Mary C Beytagh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Monica Schenone
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Chendi Li
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Audris Oh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Fei Li
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Angeliki Karatza
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Cambridge, Massachusetts
| | - Carla F Kim
- Stem Cell Program, Division of Hematology/Oncology and Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts.
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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91
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Mammalian SWI/SNF Chromatin Remodeling Complexes: Emerging Mechanisms and Therapeutic Strategies. Trends Genet 2020; 36:936-950. [PMID: 32873422 DOI: 10.1016/j.tig.2020.07.011] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
Small molecule-based targeting of chromatin regulatory factors has emerged as a promising therapeutic strategy in recent years. The development and ongoing clinical evaluation of novel agents targeting a range of chromatin regulatory processes, including DNA or histone modifiers, histone readers, and chromatin regulatory protein complexes, has inspired the field to identify and act upon the full compendium of therapeutic opportunities. Emerging studies highlight the frequent involvement of altered mammalian Switch/Sucrose-Nonfermentable (mSWI/SNF) chromatin-remodeling complexes (also called BAF complexes) in both human cancer and neurological disorders, suggesting new mechanisms and accompanying routes toward therapeutic intervention. Here, we review current approaches for direct targeting of mSWI/SNF complex structure and function and discuss settings in which aberrant mSWI/SNF biology is implicated in oncology and other diseases.
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92
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Early CA, Wangsiricharoen S, Jones RM, VandenBussche CJ. Review of SMARCA4 (BRG1)-deficient carcinomas following a malignant pleural effusion specimen confounded by reduced claudin-4 expression. J Am Soc Cytopathol 2020; 10:197-207. [PMID: 32893180 DOI: 10.1016/j.jasc.2020.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/26/2022]
Abstract
SMARCA4-deficient neoplasms are recently characterized high-grade malignancies associated with a poor prognosis. The SMARCA4 gene encodes BRG1, which is part of the SWI/SNF complex. SMARCA4-deficient neoplasms have an undifferentiated, often rhabdoid morphology, and demonstrate loss of BRG1 nuclear expression on immunohistochemistry. These neoplasms have become increasingly recognized and diagnosed in tissue specimens, but their features in cytologic specimens are poorly defined in the literature. The review is introduced by a diagnostically challenging case of a SMARCA4-deficient carcinoma involving a pleural fluid specimen in which the carcinoma cells demonstrated greatly reduced claudin-4 expression in the setting of strong, diffuse BerEP4 expression. Most of the malignant cells also demonstrated positive cytoplasmic staining for PAS and all were PAS-diastase negative, suggesting that the cytoplasm contained glycogen granules.
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Affiliation(s)
- Caroline A Early
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Robert M Jones
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher J VandenBussche
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
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93
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Xue Y, Zhu X, Meehan B, Venneti S, Martinez D, Morin G, Maïga RI, Chen H, Papadakis AI, Johnson RM, O'Sullivan MJ, Erdreich-Epstein A, Gotlieb WH, Park M, Judkins AR, Pelletier J, Foulkes WD, Rak J, Huang S. SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors. J Pathol 2020; 252:77-87. [PMID: 32558936 DOI: 10.1002/path.5493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 06/10/2020] [Indexed: 01/04/2023]
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a fatal pediatric malignancy of the central neural system lacking effective treatment options. It belongs to the rhabdoid tumor family and is usually caused by biallelic inactivation of SMARCB1, encoding a key subunit of SWI/SNF chromatin remodeling complexes. Previous studies proposed that SMARCB1 loss drives rhabdoid tumor by promoting cell cycle through activating transcription of cyclin D1 while suppressing p16. However, low cyclin D1 protein expression is observed in most ATRT patient tumors. The underlying mechanism and therapeutic implication of this molecular trait remain unknown. Here, we show that SMARCB1 loss in ATRT leads to the reduction of cyclin D1 expression by upregulating MIR17HG, a microRNA (miRNA) cluster known to generate multiple miRNAs targeting CCND1. Furthermore, we find that this cyclin D1 deficiency in ATRT results in marked in vitro and in vivo sensitivity to the CDK4/6 inhibitor palbociclib as a single agent. Our study identifies a novel genetic interaction between SMARCB1 and MIR17HG in regulating cyclin D1 in ATRT and suggests a rationale to treat ATRT patients with FDA-approved CDK4/6 inhibitors. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Brian Meehan
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sriram Venneti
- Pathology and Neuropathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel Martinez
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Rayelle I Maïga
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, PR China
| | - Andreas I Papadakis
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Radia M Johnson
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Maureen J O'Sullivan
- School of Medicine, University of Dublin, Trinity College, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Anat Erdreich-Epstein
- Departments of Pediatrics and Pathology, The Saban Research Institute at Children's Hospital Los Angeles and the Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Walter H Gotlieb
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.,Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada.,Department of Medical Genetics and Cancer Research Program, McGill University Health Centre, Montreal, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
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94
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Abstract
PURPOSE OF REVIEW Sinonasal cancers are a heterogenous group of rare cancers for which histopathological diagnosis can be very challenging and treatment options are limited for advanced disease in particular. Here, we review the candidacy of novel diagnostic and prognostic biomarkers, and therapeutic targets for sinonasal cancers. RECENT FINDINGS Molecular multidimensional analyses of sinonasal cancers have been lagging behind other major cancers, but there are numerous publications describing the discovery of novel candidate biomarkers, e.g. the methylation classifier, originally developed for brain cancers, and gene expression panels for the prediction of response to induction chemotherapy in sinonasal undifferentiated carcinoma. The most promising biomarkers are summarized and discussed further with regard to their clinical applicability and future potential. Many of the described novel biomarkers for sinonasal cancers will eventually overcome the pitfalls associated with the frequently non-specific immunohistological tests. With comprehensive, multidimensional molecular testing of these tumours in collaborative consortia projects, our better understanding of the molecular mechanisms of sinonasal cancers and their carcinogenesis will determine the most useful diagnostic and prognostic biomarkers, allow stringent multi-institutional validation and guide trials on targeted therapies.
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Affiliation(s)
- Matt Lechner
- UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
- Royal London Hospital, Barts Health NHS Trust, London, UK
- Royal National Throat, Nose and Ear Hospital/Head and Neck Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
- Royal National Throat, Nose and Ear Hospital/Head and Neck Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Valerie J Lund
- Royal National Throat, Nose and Ear Hospital/Head and Neck Centre, University College London Hospitals NHS Foundation Trust, London, UK.
- UCL Ear Institute, University College London, London, UK.
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95
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Soldi R, Ghosh Halder T, Weston A, Thode T, Drenner K, Lewis R, Kaadige MR, Srivastava S, Daniel Ampanattu S, Rodriguez del Villar R, Lang J, Vankayalapati H, Weissman B, Trent JM, Hendricks WPD, Sharma S. The novel reversible LSD1 inhibitor SP-2577 promotes anti-tumor immunity in SWItch/Sucrose-NonFermentable (SWI/SNF) complex mutated ovarian cancer. PLoS One 2020; 15:e0235705. [PMID: 32649682 PMCID: PMC7351179 DOI: 10.1371/journal.pone.0235705] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/20/2020] [Indexed: 01/01/2023] Open
Abstract
Mutations of the SWI/SNF chromatin remodeling complex occur in 20% of all human cancers, including ovarian cancer. Approximately half of ovarian clear cell carcinomas (OCCC) carry mutations in the SWI/SNF subunit ARID1A, while small cell carcinoma of the ovary hypercalcemic type (SCCOHT) presents with inactivating mutations of the SWI/SNF ATPase SMARCA4 alongside epigenetic silencing of the ATPase SMARCA2. Loss of these ATPases disrupts SWI/SNF chromatin remodeling activity and may also interfere with the function of other histone-modifying enzymes that associate with or are dependent on SWI/SNF activity. One such enzyme is lysine-specific histone demethylase 1 (LSD1/KDM1A), which regulates the chromatin landscape and gene expression by demethylating proteins such as histone H3. Cross-cancer analysis of the TCGA database shows that LSD1 is highly expressed in SWI/SNF-mutated tumors. SCCOHT and OCCC cell lines have shown sensitivity to the reversible LSD1 inhibitor SP-2577 (Seclidemstat), suggesting that SWI/SNF-deficient ovarian cancers are dependent on LSD1 activity. Moreover, it has been shown that inhibition of LSD1 stimulates interferon (IFN)-dependent anti-tumor immunity through induction of endogenous retroviral elements and may thereby overcome resistance to checkpoint blockade. In this study, we investigated the ability of SP-2577 to promote anti-tumor immunity and T-cell infiltration in SCCOHT and OCCC cell lines. We found that SP-2577 stimulated IFN-dependent anti-tumor immunity in SCCOHT and promoted the expression of PD-L1 in both SCCOHT and OCCC. Together, these findings suggest that the combination therapy of SP-2577 with checkpoint inhibitors may induce or augment immunogenic responses of SWI/SNF-mutated ovarian cancers and warrants further investigation.
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Affiliation(s)
- Raffaella Soldi
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Tithi Ghosh Halder
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Alexis Weston
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Trason Thode
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Kevin Drenner
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Rhonda Lewis
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Mohan R. Kaadige
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Shreyesi Srivastava
- HonorHealth Clinical Research Institute, Scottsdale, Arizona, United States of America
| | - Sherin Daniel Ampanattu
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Ryan Rodriguez del Villar
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Jessica Lang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | | | - Bernard Weissman
- Department of Pathology and Laboratory Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeffrey M. Trent
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - William P. D. Hendricks
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
| | - Sunil Sharma
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, Arizona, United States of America
- * E-mail:
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96
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Lee EK, Esselen KM, Kolin DL, Lee LJ, Matulonis UA, Konstantinopoulos PA. Combined CDK4/6 and PD-1 Inhibition in Refractory SMARCA4-Deficient Small-Cell Carcinoma of the Ovary, Hypercalcemic Type. JCO Precis Oncol 2020; 4:736-742. [PMID: 32704608 PMCID: PMC7377332 DOI: 10.1200/po.20.00063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2020] [Indexed: 01/05/2023] Open
Affiliation(s)
- Elizabeth K Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Katharine M Esselen
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA
| | - David L Kolin
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Boston, MA
| | - Larissa J Lee
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Hospital Cancer Center, Boston, MA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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97
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Schaefer IM, Hornick JL. SWI/SNF complex-deficient soft tissue neoplasms: An update. Semin Diagn Pathol 2020; 38:222-231. [PMID: 32646614 DOI: 10.1053/j.semdp.2020.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 01/04/2023]
Abstract
The SWItch Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex is a large multi-subunit protein assembly that orchestrates chromatin compaction and accessibility for gene transcription in an ATP-dependent manner. As a key epigenetic regulator, the SWI/SNF complex coordinates gene expression, cell proliferation and differentiation, and its biologic functions, in part, antagonize the polycomb repressive complex 2. The mammalian SWI/SNF complex consists of 15 subunits encoded by 29 genes, some of which are recurrently mutated in human cancers, in the germline or sporadic setting. Most SWI/SNF-deficient tumors share common "rhabdoid" cytomorphology. SMARCB1 (INI1) is the subunit most frequently inactivated in soft tissue neoplasms. Specifically, SMARCB1 deficiency is observed as the genetic hallmark in virtually all malignant rhabdoid tumors, and most cases of epithelioid sarcoma and poorly differentiated chordoma. In addition, subsets of myoepithelial carcinoma (10-40%), extraskeletal myxoid chondrosarcoma (20%), epithelioid schwannoma (40%), and epithelioid malignant peripheral nerve sheath tumor (70%) demonstrate SMARCB1 loss. The gene encoding the SS18 subunit is involved in the SS18-SSX rearrangement, which is pathognomonic of synovial sarcoma and indirectly inactivates SMARCB1. Finally, undifferentiated SMARCA4-deficient thoracic sarcomas are defined by SMARCA4 subunit inactivation, leading to SMARCA4 and SMARCA2 loss. Rarely, inactivation of alternate but biologically equivalent key regulators can substitute for canonical subunit deficiency, such as SMARCA4 inactivation in cases of SMARCB1-retained epithelioid sarcoma. This review briefly highlights SWI/SNF complex biologic functions and its roles in human cancer and provides a detailed update on recent advances in soft tissue neoplasms with canonical SWI/SNF complex deficiency, correlating morphologic, genomic, and immunohistochemical findings.
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Affiliation(s)
- Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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98
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Iijima Y, Sakakibara R, Ishizuka M, Honda T, Shirai T, Okamoto T, Tateishi T, Sakashita H, Tamaoka M, Takemoto A, Kumaki Y, Ikeda S, Miyazaki Y. Notable response to nivolumab during the treatment of SMARCA4-deficient thoracic sarcoma: a case report. Immunotherapy 2020; 12:563-569. [PMID: 32363992 DOI: 10.2217/imt-2019-0142] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
SMARCA4-deficient thoracic sarcoma is a rare tumor typically presenting as a mediastinal mass. The prognosis is estimated to be poor, and no effective treatment has been established. We present a case of a 76-year-old man who was diagnosed with SMARCA4-deficient thoracic sarcoma. The provisional diagnosis was carcinoma of unknown primary but subsequently corrected to SMARCA4-deficient thoracic sarcoma based on the panel-based cancer gene screening and immunohistochemistry. Cytotoxic chemotherapy as the first- and second-line did not reveal enough therapeutic effects but third-line therapy using nivolumab showed marked tumor regression, which was sustained. This is the first case report of SMARCA4-deficient thoracic sarcoma showing a good response to nivolumab. Immune checkpoint inhibitor might be therapeutic candidates for this type of tumor.
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Affiliation(s)
- Yuki Iijima
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Rie Sakakibara
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Masahiro Ishizuka
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takayuki Honda
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Tsuyoshi Shirai
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Tsukasa Okamoto
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Tomoya Tateishi
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Hiroyuki Sakashita
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan.,Cancer Center, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Meiyo Tamaoka
- The Department of Respiratory Medicine, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Akira Takemoto
- The Department of Pathology, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yuichi Kumaki
- Cancer Center, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Sadakatsu Ikeda
- Cancer Center, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yasunari Miyazaki
- Cancer Center, Tokyo Medical & Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
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99
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van der Vaart A, Godfrey M, Portegijs V, van den Heuvel S. Dose-dependent functions of SWI/SNF BAF in permitting and inhibiting cell proliferation in vivo. SCIENCE ADVANCES 2020; 6:eaay3823. [PMID: 32494730 PMCID: PMC7250657 DOI: 10.1126/sciadv.aay3823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/09/2020] [Indexed: 05/14/2023]
Abstract
SWI/SNF (switch/sucrose nonfermenting) complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb group (PcG) proteins. Genes encoding SWI/SNF components are critical for normal development and frequently mutated in human cancer. We characterized the in vivo contributions of SWI/SNF and PcG complexes to proliferation-differentiation decisions, making use of the reproducible development of the nematode Caenorhabditis elegans. RNA interference, lineage-specific gene knockout, and targeted degradation of SWI/SNF BAF components induced either overproliferation or acute proliferation arrest of precursor cells, depending on residual protein levels. Our data show that a high SWI/SNF BAF dosage is needed to arrest cell division during differentiation and to oppose PcG-mediated repression. In contrast, a low SWI/SNF protein level is necessary to sustain cell proliferation and hyperplasia, even when PcG repression is blocked. These observations show that incomplete inactivation of SWI/SNF components can eliminate a tumor-suppressor activity while maintaining an essential transcription regulatory function.
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Affiliation(s)
| | | | - Vincent Portegijs
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
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The SWI/SNF complex in cancer - biology, biomarkers and therapy. Nat Rev Clin Oncol 2020; 17:435-448. [PMID: 32303701 DOI: 10.1038/s41571-020-0357-3] [Citation(s) in RCA: 322] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 12/11/2022]
Abstract
Cancer genome-sequencing studies have revealed a remarkably high prevalence of mutations in genes encoding subunits of the SWI/SNF chromatin-remodelling complexes, with nearly 25% of all cancers harbouring aberrations in one or more of these genes. A role for such aberrations in tumorigenesis is evidenced by cancer predisposition in both carriers of germline loss-of-function mutations and genetically engineered mouse models with inactivation of any of several SWI/SNF subunits. Whereas many of the most frequently mutated oncogenes and tumour-suppressor genes have been studied for several decades, the cancer-promoting role of mutations in SWI/SNF genes has been recognized only more recently, and thus comparatively less is known about these alterations. Consequently, increasing research interest is being focused on understanding the prognostic and, in particular, the potential therapeutic implications of mutations in genes encoding SWI/SNF subunits. Herein, we review the burgeoning data on the mechanisms by which mutations affecting SWI/SNF complexes promote cancer and describe promising emerging opportunities for targeted therapy, including immunotherapy with immune-checkpoint inhibitors, presented by these mutations. We also highlight ongoing clinical trials open specifically to patients with cancers harbouring mutations in certain SWI/SNF genes.
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